tbuckley/cabot-search huggingface dataset:
A next-generation sequencing methylation assay for sub-typing small cell lung cancer in cell-free DNA.
Authors: chung-Ying Huang, Ashley D. Berkebile, Allison Parker, Jennifer Hernandez, Frazer Meacham, Kavita Garg, Jiannan Guo
Journal: Journal of Clinical Oncology (2023)

e15021 Background: Liquid biopsy provides an easy access and minimally invasive technique to inform cancer patient management in clinics as well as clinical trials. Detecting genomic alterations in circulating tumor DNA (ctDNA) has demonstrated clinical utility and actionability in therapy selection and longitudinal monitoring. The development of a comprehensive assay that provides multi-omic information is imperative to expand the utility of liquid biopsy. Methods: Agilent Resolution ctDNA diagnostic assays can detect all four major types of actionable genomic alterations for cancer patients: SNVs, Indels, fusions, and CNVs. The Agilent Resolution ctDx FIRST assay has recently been approved by the FDA as a companion diagnostic assay for non-small cell lung cancer (NSCLC). Applying the same core technology, we developed an additional assay that enables methylation profiling in cfDNA. The custom methylation-specific panel targets informative regions to detect tumor signals and potentially profile the disease by subtype. Recent reports suggest that small cell lung cancer (SCLC) may be stratified into subtypes based on gene expression, including that of ASCL-1, NEUROD1, and POU2F3. We used the proposed SCLC subtyping model to test the feasibility of subtyping SCLC by cfDNA methylation profiles. A baseline methylation profile was established using cell-free DNA from healthy donors. Test samples included genomic DNA from SCLC cell lines and plasma samples of SCLC patients with matching tissue, where available. Results: We applied a methylation-specific bioinformatic pipeline that generates error-corrected unique molecules. The methylation workflow showed unique coverage comparable to our ctDx assay and produced consistent results from input DNA as low as 1ng. We found consistent methylation patterns in cfDNA among healthy donors. SCLC cell lines showed distinct profiles that could be classified into sub-types. When spiked into healthy donor cfDNA background, the tumor signals were distinguishable down to ~0.5%. Plasma samples from SCLC patients showed profiles consistent with that of SCLC sub-types defined by cell lines. Matching plasma and tissue samples produced concordant sub-typing results, supporting the feasibility of disease subtyping in both sample types. Samples were also tested by a custom SCLC panel to analyze genomic alterations. Prevalent variants in SCLC were detected, including SNVs in TP53, PIK3CA, RB1, and MYC amplifications. Conclusions: We showed a cfDNA methylation profiling platform that could support disease sub-typing for SCLC. This platform has great potential in disease stratification and patient management.
Dual inhibition of PARP and ATR induces homologous recombination repair deficiency and leads to synthetic lethality in prostate cancer with <i>CDK12</i> alteration.
Authors: Shusuke Akamatsu, Yuki Kamiyama, Takuro Sunada, Kensuke Hikami, Tomohiro Fukui, Kei Mizuno, Takayuki Sumiyoshi, Takayuki Goto, Takashi Kobayashi, Hiroyuki Sasanuma
Journal: Journal of Clinical Oncology (2023)

e17042 Background: CDK12 is considered as a gene involved in homologous recombination repair (HRR); however, recent clinical trials have shown poor benefit of poly(ADP-ribose) polymerase(PARP) inhibitors in prostate cancer (PCa) patients with CDK12 alterations. Since CDK12 is the third most commonly altered gene in the HRR pathway in PCa, development of a new treatment strategy is urgently needed. Methods: To understand the biological consequence of CDK12 alteration, CDK12 was knocked out in LNCaP using CRISPR-Cas9 system to generate CDK12KO cells. Cell growth and cell cycle were evaluated as well as HRR efficiency. Downstream genes were evaluated by RT-PCR and western blots. Combination therapy by a PARP inhibitor and ATR inhibitors were tested using two lines of patient derived xenografts (PDX) established from tissues of patients with deleterious CDK12 variants. Three different ATR inhibitors were tested to confirm reproducibility. Results: In LNCaP, CDK12 knockout enhanced cell cycle progression until the M phase, however, cell cycle was stalled at the M phase with accumulation chromosomal aberration, suggesting that rapidly progressive CDK12 altered tumors clinically encountered harbor a mechanism of escaping the M phase checkpoint without DNA repair. γH2AX was accumulated in CDK12KO after treatment with CPT11, consistent with impaired HRR in CDK12 KO cells. Analysis of HRR associated genes showed that in PCa, CDK12 knockout leads to transcriptional downregulation of ATM but not the other HRR associated genes. Expression patterns of downstream genes after double strand break (DSB) induction in CDK12 and ATM knockout cells suggested that in PCa, CDK12 regulates HRR through regulation of ATM. Since synthetic lethality of PARP and ATR inhibition has been reported in ATM deficient PCa, 2 PDX lines with CDK12 alterations were administered the combination therapy. Tumor growth suppression and accumulation of γH2AX in tumor tissue was observed when treated by the combination therapy, but not with either drug alone. Either drug alone or in combination did not affect the growth of a PDX established from a tissue of a patient with wild-type CDK12. Conclusions: In PCa, CDK12 acts through transcriptional regulation of ATM, and combination treatment with PARP inhibitor and ATR inhibitor could be a potential treatment strategy in PCa with CDK12 alteration.
Adjuvant therapy in localized vs regional biliary tract cancers: A SEER analysis.
Authors: John X Wei, Christina Wang, Sofya Pintova
Journal: Journal of Clinical Oncology (2023)

e16221 Background: Biliary Tract Cancers (BTC) are aggressive malignancies. Treatment of early-stage disease involves surgical resection, but whether adjuvant therapy offers a clear survival benefit remains inconclusive. This study aims to explore the impact of demographic factors and adjuvant therapy on survival outcomes at a population level through the lens of the latest SEER (Surveillance, Epidemiology, and End Results) registries. Methods: Cases were filtered by the following criteria: histologic type (adenocarcinoma), anatomic location (gallbladder, intrahepatic, extrahepatic), stage (local and regional), microscopically confirmed diagnosis, and confirmed surgical resection. Cases with incomplete entries were excluded. A Cox proportional hazard model was used to analyze survival in the context of race, gender, income, and type of adjuvant therapy (none, chemotherapy (AC), chemo-radiotherapy (CRT), and radiation (RT)). Data analysis was performed in RStudio. Results: Between 2005 and 2019, 3565 patients were identified. Patients with regional BTC demonstrated improved median survival with AC (27 vs 23 months, HR 0.72, CI 0.63-0.82, p ≤.05) and CRT (28 vs 23 months, HR 0.63, CI 0.56-0.72, p ≤.05). Median survival in localized BTC was 52 months. Adjuvant therapy of any type did not impact survival for localized BTC. Analysis of race as a covariate in localized BTC showed that all minority groups had improved survival compared to non-Hispanic whites (Asian, HR 0.33; Black, HR 0.50; Hispanic, HR 0.38, p≤.05). In regional gallbladder BTC, this survival benefit was limited to Asians only (HR 0.52, p≤.05). Conclusions: Our data show that AC and CRT may improve survival in patients with regional BTC across all anatomic subtypes. In our cohort, adjuvant therapy had no impact on survival in localized BTC. Differences in outcomes may exist among racial groups for different subtypes of BTC. Future adjuvant clinical trials for BTC should consider stratifying for regional and localized disease. [Table: see text]
Effect of KDR mutations on efficacy of immune checkpoint inhibitors in patients with bladder cancer.
Authors: Honghai Dai, Qin Zhang, Yuan Tan, Qianqian Duan
Journal: Journal of Clinical Oncology (2023)

4521 Background: KDR (kinase insert domain receptor) is the most important VEGF (vascular endothelial growth factor) receptor that mediates the signaling transduction initiated by the VEGF ligands. VEGF signaling can activate angiogenesis which plays a crucial role in tumor growth, metastasis, and treatment response. Here we explore the relationship between KDR mutation and its efficacy of immune checkpoint inhibitors (ICIs) in patients with bladder cancer. Methods: To explore the association between KDR mutations and the efficacy of ICIs in bladder cancer patients, we collected clinical and mutation data of 215 patients who received ICIs (PD-(L)1 and/or CTLA-4 inhibitors) from MSKCC cohort. Gene expression data and WES mutation data of 413 samples in the TCGA database were obtained from the UCSC Xena for analysis of the differences of potential biological mechanisms between KDR-mutant and KDR-wildtype tumors. TMB was calculated as the total number of somatic non-synonymous mutations per megabase. CIBERSORT was applied to infer 22 immune cell type proportions in TCGA advanced bladder cancers. Results: In MSKCC cohort, we observed 5.6% (12/215) samples had KDR mutation. Survival analysis showed that KDR-mutant patients had longer overall survival (OS) than that of wildtype patients (hazard ratio (HR) = 0.27, 95% CI: 0.07-1.09, logrank test P = 0.048); median OS (not reached versus 15 months). Then we compared the TMB between KDR-mutant and KDR-wildtype tumors, the results showed that KDR-mutant group had higher TMB in MSKCC cohort (median [IQR]: 17.58 [11.64–47.81] versus 7.90 [4.92–14.76], P=0.002) and TCGA cohort (median [IQR]: 10.69 [5.87–19.85] versus 4.60 [2.52–8.08], P=0.001). Analysis of 22 immune cell subsets in the TCGA advanced bladder cancers, B cells naive, plasma cells and macrophages M1 were significantly abundant in KDR-mutant tumors (all P &lt;0.05). Conclusions: In ICI-treated bladder cancers, KDR mutation is associated with prolonged OS, higher TMB and activated antitumor immunity, which suggests that KDR mutation may serve as a potential biomarker to guide ICI therapy in bladder cancer.
Recurrence free survival in patients with HPV+ head and neck cancer treated with TORS and neck dissection.
Authors: Manasa Melachuri, Terral Patel, Daniel Awad, Seungwon Kim, Shaum Sridharan, Umamaheswar Duvvuri
Journal: Journal of Clinical Oncology (2023)

e18076 Background: Prior research has demonstrated that delays to initiation of radiation therapy (RT) in the treatment of head and neck squamous cell carcinoma (HNSCC) after surgery result in poorer survival outcomes. However, there is limited data with little long-term follow up to evaluate whether human papilloma virus (HPV) positive primaries undergoing transoral robotic surgery (TORS) and neck dissection (ND) face a similar decrement in recurrence free survival (RFS) and disease specific survival (DSS). Methods: Single center retrospective chart review of patients diagnosed with HPV positive primary nonmetastatic HNSCC who underwent TORS with ND followed by RT with or without Chemotherapy and/or Immunotherapy from 2012-2022 with data collection from December 2022 to February 2023. 248 patients met inclusion criteria and were analyzed for DSS and RFS. Kaplan-Meier survival analysis with Log-rank testing was used to assess the impact of time intervals between diagnosis, TORS, radiation initiation and radiation completion on survival. Univariable and Multivariable Cox proportional hazards regression analysis was performed to identify factors associated with RFS and DSS and adjust for potential confounding variables. Subgroup analysis was completed with high risk (lymph nodes &gt; 4 with extracapsular extension) and low risk population. Results: Median follow-up time was 47.22 months (1452.07 days). Of 248 patients, 17 had a recurrence and 12 died due to disease. In patients who underwent radiation therapy for a time frame (T R1-R2 ) of 5-7 weeks compared with those who had a shortened or prolonged course of RT, RFS (140.116 months, p-value = .012) and DSS (142.641 months, p-value = .016) were improved. Although time from diagnosis to TORS did not impact RFS (p-value = .195), improved RFS persisted in patients who underwent time from diagnosis to radiation completion (T D-R2 ) or total treatment package time (TTPT) between 17-20 weeks (109.155 months, 95% CI: 105.276-113.034, p-value = .057) compared to patients with TTPT less than 17 or greater than 20 weeks. When the population is stratified into high risk and low risk groups, patients in the high risk group who underwent Chemotherapy had improved RFS compared to no chemotherapy (HR: 7.19, p-value = .09). On Univariate Analysis, T R1-R2 &lt; 5 weeks and &gt; 7 weeks, T D-R2 &lt; 17 weeks and &gt; 20 weeks, extracapsular extension, smoking history, and age &gt; 70 were associated with increased risk of recurrence. Conclusions: For HPV positive patients with OPSCC undergoing TORS and Neck dissection, time to radiation initiation may not be as critical in improving OS, DSS, and RFS as other patient populations. However, the length of radiation time between 5 to 7 weeks and overall treatment time from 17-20 weeks may improve recurrence free survival and disease specific survival.
Neutrophil-to-lymphocyte ratio as a predictor of immune checkpoint inhibitor therapy response in advanced bladder cancer.
Authors: Monica Nair, Scott Dawsey, Nikhil Pramod, Jean Rene Clemenceau, Timothy D. Gilligan, Moshe Chaim Ornstein, Christopher Eing Wee, Amanda Nizam, Nima Almassi, Christopher J. Weight, Michi Gray, Jessica Echle, Jay P. Ciezki, Kevin L. Stephans, Rahul D. Tendulkar, Jacob Scott, Shilpa Gupta, Omar Y. Mian
Journal: Journal of Clinical Oncology (2023)

e16586 Background: Immune checkpoint inhibitor (ICI) therapy is a novel and promising agent for treating muscle invasive bladder cancer (MIBC). However, there is a need for further understanding of which patient factors or biological markers can be used to help identify patients who will have a successful response to ICI therapy. We hypothesized that Neutrophil-to-Lymphocyte Ratio (NLR) could be predictive of response to ICI therapy as this ratio has previously been reported to correlate with a higher number of myeloid derived suppressor cells. Methods: A retrospective cohort analysis was performed on patients with advanced or metastatic bladder cancer who were treated with ICI therapy at a single institution between 2015-2020. Information on survival, disease recurrence, and patient characteristics was gathered. Neutrophil and lymphocyte numbers were recorded at time of ICI administration and a ratio of neutrophils to lymphocytes was calculated. The median of these values was calculated and used to divide the cohort into low NLR and high NLR. Tissue samples from a subset of these patients were collected and sent for multiplex immunohistochemistry with a myeloid and T cell staining panel. Results: In a cohort of 115 patients with advanced bladder cancer treated with ICI, the mean time to last follow up or event (death or disease progression) was 375.78 days (SD 41). 35 patients (30%) had either a complete or partial response to ICI therapy. A Kaplan Meier survival analysis shows a significant difference in survival between the low and high NLR group, with lower NLR having a longer event free survival (Wilcoxon rank p = 0.0156). Multiplex IHC showed variable tumor and adjacent microenvironmental distributions of myeloid and lymphoid marker positive populations in ICI responders and non-responders. Conclusions: In an effort to better predict which patients may benefit from ICI therapy, we have studied NLR at the time of ICI administration and its association with event free survival. Our results suggest that a lower NLR could be associated with a longer event free survival. Further research is being conducted to study the immune microenvironment as it relates to bladder cancer response to ICI therapy.
Optimization of protein extraction for proteomic analysis of formalin-fixed and paraffin-embedding (FFPE) biopsy specimens from males with breast cancer.
Authors: Maria Júlia Barbosa Bezerra, Jackeline Almeida Silva, Rosane Oliveira Sant'Ana, Clarissa Gondim Picanço-Albuquerque, Maria Claudia dos Santos Luciano, Jose Fernando Bastos, Francisca Fernanda Barbosa Oliveira, Italo Aguiar Freire, Flávio da Silveira Bitencourt, Carlos Gustavo Hirth, Paulo Goberlanio de Barros Silva, Isabelle Joyce de Lima Silva-Fernandes
Journal: Journal of Clinical Oncology (2023)

e13119 Background: Male breast cancer corresponds to 1% of breast cancer diagnoses. Given this low incidence, the tumors detected have a worse prognosis and lethality. Formalin fixation and paraffin-embedding (FFPE) methods are the most common to maintain biopsied samples. It is a low-cost procedure and is a valuable resource for the study of pathological molecular mechanisms and research of potential biomarkers and therapeutic target molecules. However, in this technique cross-links are formed compromising protein extraction, resulting in low yield and quality for mass spectrometry analysis. Objective: To present an optimized method of protein extraction from male breast FFPE samples for proteomic analysis. Methods: Four protein extraction protocols were optimized and tested in female breast cancer FFPE samples from Haroldo Juaçaba Hospital/Cancer Institute of Ceará to preserve the male sample. Each protocol was performed using a total of eight 5uM tumor slides. Different deparaffinization processes were tested followed by distinct extraction buffers and variable incubation time. The characteristics of each of the protocols and optimizations are presented in the table. The quantification of the protein profile was carried out in nanodrop 2000. The protocol with the highest yield was used in the male breast cancer sample FFPE. Analysis of the protein profile in polyacrylamide gel (SDS PAGE) was performed. Results: Protocol IV presented the highest yield of protein (16.9 mg/mL) and protocols I, II, and III presented, 0.46 mg/mL and 0.28 mg/ml, and 2.3 mg/mL, respectively. Protocol IV was selected to be used in the male breast cancer sample and the yield was 14.26 mg/mL, similar to the female sample. Protein bands from male and female samples using protocol IV were detected on the SDS-PAGE gel. Conclusions: Protocol IV performed a satisfactory protein yield in breast cancer samples FFPE. [Table: see text]
Incidence of non-canonical IDH mutations and IDH co-mutations in a multicenter prospective study of patients with glioma.
Authors: Santiago Cabezas-Camarero, Rebeca Pérez-Alfayate, Vanesa García-Barberán, Marisa Gandía, Pablo García-Feijoo, Igor López-Cade, Isabel Casado-Fariñas, Mario Garcia-Conde, Yanire Sanchez-Medina, Maria Angeles Ceron, Miguel Sotelo Lezama, Pedro Pérez-Segura
Journal: Journal of Clinical Oncology (2023)

e14033 Background: IDH-mutant tumors are a distinct disease entity accounting for one third of gliomas with a more favourable prognosis despite still harboring high morbidity and mortality rates. Most IDH mutations (muts) in gliomas group at R132/R172 hotspots in IDH1/IDH2, respectively. Our aim was to study IDH non-canonical muts and IDH co-mutations (co-muts) since the evidence is still limited. Methods: Prospective study of patients (pts) with gliomas at 4 third-level hospitals in Spain (Hospital Clinico Universitario San Carlos, Hospital Universitario La Paz, Hospital Universitario de Canarias, Hospital Universitario Nuestra Señora de la Candelaria). High throughput next generation sequencing (NGS) using a customized gene panel ((Illumina, Inc) including IDH1 and IDH2 was used in FFPE and/or fresh tumor samples, and run in an Illumina MiSeq instrument (Illumina, Inc). Only pathogenic mutations were considered as valid. Clonal IDH (cIDH) muts were defined as those with a MAF ≥ 1% and subclonal IDH (scIDH) muts as those with a MAF &lt; 1%. Results: Between February 2017 and February 2021, 49 glioma pts enrolled and sequenced for IDH1/IDH2 tumor muts. Median age 51 (Min-max: 20-78). WHO 5th Ed (n = 42): IDH-MUT astrocytoma (n = 14), IDH-MUT oligodendroglioma (n = 7), IDH-WT glioblastoma (n = 21). 37/49 pts (75.5%) presented cIDH and/or scIDH muts, of which 21 pts (43%) harbored cIDH muts in IDH1 (R132H (n = 17), R132C (n = 1), R132G (n = 1), R100Q (n = 1), G161R (n = 1)) and in IDH2 (R140W (n = 1), R140Q (n = 1)). In 17/21 pts (81%) cIDH-mut MAF ≥ 10%. Of 21 cIDH-mutant pts, there were IDH co-muts in 11 pts (52%). Of these 11 pts, IDH co-muts were scIDH in 91%: #2 (IDH1 R100Q/G161R), #3 (IDH1 R132H/R119Q/G161R), #4 (IDH1 R132H/R132C; IDH2 R172G/R140Q), #11 (IDH1 R132H/R132C), #21 (IDH1 R132H/G161R; IDH2 R140Q), #23 (IDH1 R132H/R132C), #31 (IDH1 R132H/G161R; IDH2 R140Q/P162L), #32 (IDH1 R132H/R100Q), #33 (IDH1 R132H/R100Afs*29/I130V), #37 (IDH1 R132H; IDH2 R159H), #40 (IDH1 R132H; IDH2 R172G). Median overall survival (OS) longer in cIDH-mut vs IDH-wt (159 vs 16 months, P = 0.000). No difference in OS in: cIDH vs cIDH + scIDH (NR vs 67 m, P = 0.437), in scIDH vs cIDH (79 vs 159 m, P = 0.111), and scIDH vs IDH-wt (79 vs 12 m, P = 0.229). Conclusions: Subclonal (defined as MAF &lt; 1%) canonical and non-canonical IDH-mutations and co-mutations occur frequently in gliomas. This may have implications for the design of future clinical trials and in the development of IDH inhibitors including the anticipation of potential resistance mechanisms.
Health related quality of life (HRQoL) in patients with triple-class-exposed relapsed/refractory multiple myeloma (TCE RRMM) treated with idecabtagene vicleucel (ide-cel) versus standard regimens: Patient-reported outcomes (PROs) from KarMMa-3 phase 3 randomized controlled trial (RCT).
Authors: Michel Delforge, Krina K. Patel, Laurie Eliason, Devender Dhanda, Ling Shi, Shien Guo, Thomas Marshall, Bertrand Arnulf, Michele Cavo, Ajay K. Nooka, Salomon Manier, Natalie Scott Callander, Sergio Giralt, Hermann Einsele, Sikander Ailawadhi, Mihaela Popa McKiver, Mark Cook, Paula Rodríguez-Otero
Journal: Journal of Clinical Oncology (2023)

8032 Background: Patients (pts) with TCE RRMM have few treatment (Tx) options and poor HRQoL. Ide-cel, the first in class CAR T cell Tx for pts with TCE RRMM, improved PFS versus standard (std) regimens in the KarMMa-3 trial. We report the PRO results comparing the Tx arms. PROs provide further understanding of Tx benefit of ide-cel from the pts’ perspective. Methods: KarMMa-3 (NCT03651128) is an open-label phase 3 RCT comparing the efficacy and safety of ide-cel with std regimens in pts with TCE RRMM, who had received 2–4 prior regimens. In addition to clinical endpoints, we evaluated the impact of ide-cel compared with std regimens on the changes in HRQoL, measured by the EORTC QLQ-C30, EORTC QLQ-MY20, and the EQ-5D-5L questionnaires. PROs were collected at baseline (screening), day of infusion and monthly from 2–24 months (mo) and thereafter every 3 mo. This interim analysis reports PROs through 20 mo. Comparisons were performed on least squares mean (LSM) changes from baseline over time between arms using constrained longitudinal data analysis (cLDA). Results: In total, 386 pts were randomized (ide-cel, 254; std regimens, 132). PRO compliance was high over time ( &gt; 80%). At baseline, PROs were similar between arms. LSM changes from baseline to 20 mo showed significant differences ( P &lt; 0.05), with effect sizes of 0.3–0.7, in favor of ide-cel for most domains, including global health status/QoL, cognitive functioning, fatigue, and pain (EORTC QLQ-C30); side effects of Tx (EORTC QLQ-MY20); and the EQ-5D-5L VAS. The difference in overall LSM change reached or exceeded the pre-specified between-groups minimal importance difference (MID) for improvement in most domains in favor of ide-cel (Table). Conclusions: Ide-cel showed statistically significant and clinically meaningful improvements in HRQoL, including key MM symptoms and functioning, for pts with TCE RRMM compared with std regimens. The PRO data for ide-cel expands upon the clinical outcomes observed in the KarMMa-3 trial. Clinical trial information: NCT03651128 . [Table: see text]